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- PDB-5ddv: Crystal structure of IspD from Bacillus subtilis at 2.30 Angstrom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ddv | ||||||
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Title | Crystal structure of IspD from Bacillus subtilis at 2.30 Angstroms resolution, crystal form II | ||||||
![]() | 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jin, Y. / Liu, Z.C. / Wang, G.G. | ||||||
![]() | ![]() Title: A structural and functional study on the 2-C-methyl-d-erythritol-4-phosphate cytidyltransferase (IspD) from Bacillus subtilis. Authors: Jin, Y. / Liu, Z. / Li, Y. / Liu, W. / Tao, Y. / Wang, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 41.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.6 KB | Display | ![]() |
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Full document | ![]() | 428.4 KB | Display | |
Data in XML | ![]() | 10.6 KB | Display | |
Data in CIF | ![]() | 14 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ddtC ![]() 5hs2C ![]() 2yc3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25879.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 168 / Gene: ispD, yacM, BSU00900 / Plasmid: pGEX-6P-1 / Production host: ![]() ![]() References: UniProt: Q06755, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M HEPES pH7.5, 25% (v/v) Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. obs: 11687 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.9 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YC3 Resolution: 2.3→51.53 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 8.429 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.023 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→51.53 Å
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Refine LS restraints |
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